rs1194707294

Variant names:

• chr19-11030756-A-C
• NM_001387283.1:c.3409A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-11030756-A-C
• chr19-11030756-A-G
• chr19-11030756-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 5P and 2B. PM1 PM2 PP2 BP4_Moderate

The NM_003072.5(SMARCA4):​c.3409A>C​(p.Met1137Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SMARCA4 NM_003072.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.55

Genes affected

SMARCA4 (HGNC:11100): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM1: In a domain Helicase C-terminal (size 162) in uniprot entity SMCA4_HUMAN there are 12 pathogenic changes around while only 0 benign (100%) in NM_003072.5
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the SMARCA4 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 59 curated pathogenic missense variants (we use a threshold of 10). The gene has 56 curated benign missense variants. Gene score misZ: 6.8459 (above the threshold of 3.09). Trascript score misZ: 8.7957 (above the threshold of 3.09). GenCC associations: The gene is linked to uterine corpus sarcoma, Coffin-Siris syndrome 1, intellectual disability, autosomal dominant 16, rhabdoid tumor predisposition syndrome 2, familial rhabdoid tumor, hereditary nonpolyposis colon cancer, Coffin-Siris syndrome.
• BP4: Computational evidence support a benign effect (MetaRNN=0.19719821).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3409A>C	p.Met1137Leu	missense_variant	Exon 26 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3409A>C	p.Met1137Leu	missense_variant	Exon 25 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3409A>C	p.Met1137Leu	missense_variant	Exon 26 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.2821A>C	p.Met941Leu	missense_variant	Exon 22 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2053A>C	p.Met685Leu	missense_variant	Exon 18 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.2134A>C	p.Met712Leu	missense_variant	Exon 18 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.1894A>C	p.Met632Leu	missense_variant	Exon 17 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.1762A>C	p.Met588Leu	missense_variant	Exon 16 of 25			ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1

Mar 07, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.M1137L variant (also known as c.3409A>C), located in coding exon 24 of the SMARCA4 gene, results from an A to C substitution at nucleotide position 3409. The methionine at codon 1137 is replaced by leucine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Missense and in-frame variants in SMARCA4 are known to cause neurodevelopmental disorders; however, such associations with rhabdoid tumor predisposition syndrome including small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) are exceedingly rare (Kosho T et al. Am J Med Genet C Semin Med Genet. 2014 Sep;166C(3):262-75; Jelinic P et al. Nat Genet. 2014 May;46(5):424-6). Based on the supporting evidence, the association of this alteration with Coffin-Siris syndrome is unknown; however, the association of this alteration with rhabdoid tumor predisposition syndrome is unlikely. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.012	T
BayesDel_noAF	Benign	-0.25
CADD	Uncertain	24
DANN	Benign	0.97
DEOGEN2	Uncertain	0.48	T;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;T;.;.;.
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.11
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D;D;D;D
M_CAP	Benign	0.053	D
MetaRNN	Benign	0.20	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.81	T
MutationAssessor	Benign	-0.57	N;.;.;.;N;N;.;N;N;N;N;N;N;N;N;N;.;.;.;.;.
PrimateAI	Uncertain	0.79	T
PROVEAN	Benign	-1.3	N;.;.;.;.;.;.;.;.;.;N;.;N;.;N;.;.;N;.;.;.
REVEL	Benign	0.24
Sift	Benign	0.22	T;.;.;.;.;.;.;.;.;.;T;.;T;.;T;.;.;T;.;.;.
Sift4G	Benign	0.25	T;.;.;.;.;.;.;.;.;.;T;.;T;T;T;T;T;T;.;.;.
Polyphen		0.0020	B;.;B;.;.;.;.;.;.;.;B;.;.;.;.;.;.;B;.;.;.
Vest4		0.49
MutPred		0.36		Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);Loss of ubiquitination at K1140 (P = 0.1151);.;Loss of ubiquitination at K1140 (P = 0.1151);.;.;.;
MVP		0.61
MPC		1.6
ClinPred		0.74	D
GERP RS		4.6
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.7
Varity_R		0.28
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-11141432;